you have to balance any small hints with the very obvious fact that he has created paradise out of hell on earth. Michonne didn't exactly give a lot of details about why she was uncomfortable there.

I think she said enough, on top of things/behavor happening in front of Andrea's face.

And she isn't exactly normal.

Part of that is survivor's instinct, and she was correct in assuming the fresh blood on the national guard vehicles meant the governor's men murdered the guards--that says much about that town.

Even if she did not discover that, for all we know, her immediate questioning/suspicion of the governor's town may be due to whatever past experiences she had with survivors. From the season two bar fight involving the strangers vs. Rick, Hershel and Glenn, we know there are roaming, predatory types in that world, so it is not a stretch to think Michonne has run into that before.

And Andrea's own group was pretty crazy too. You also need to consider the fact that they are all traumatized and in mourning.

If you start with the group from early in seaon one, remove Merle, Shane and Carol's husband, and the group was pretty average in behavior.

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"...to be like God, you have the power to make the world anything you want it to be."